prepared shiny app scripts for execution

OdyOSG · Mar 8, 2024 · 789f5c9 · 789f5c9
1 parent 6cde002
commit 789f5c9
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 18 deletions.
diff --git a/shiny/R/fn.R b/shiny/R/fn.R
@@ -223,7 +223,6 @@ plotKM2 <- function(dat) {
   plot_colors <- unname(grafify::graf_palettes$kelly)
 
   p <- ggplot(dat, aes(x = time, y = estimate, color = outcomeCohortId)) +
-    #ggsurvfit::add_risktable(risktable_stats = c("n.risk", "cum.censor", "cum.event")) +   ## ADDED
     geom_step(linewidth = 1.5) +
     scale_color_manual(values = plot_colors) + #scale colors to kelly
     scale_y_continuous(labels = scales::percent_format()) + # convert y axis to percent

diff --git a/shiny/R/loadData.R b/shiny/R/loadData.R
@@ -8,7 +8,7 @@ library(readr)
 source(here::here("shiny", "R", "fn.R"))
 source(here::here("shiny", "migration", "helpers.R"))
 
-dataPath <- here::here("shiny", "data_0603")
+dataPath <- here::here("shiny", "data")
 
 
 # About -----------------

diff --git a/shiny/migration/dataMigration.R b/shiny/migration/dataMigration.R
@@ -7,11 +7,11 @@ library(readr)
 source("shiny/migration/helpers.R")
 
 
-appDataPath <- here::here("shiny", "data_0603") # Path to place app data
+appDataPath <- here::here("shiny", "data") # Path to place app data
 
 appDataPath %>% fs::dir_create() # Create new directory
 
-resultsPath <- here::here("results_0603") # Set path to the execution results
+resultsPath <- here::here("results") # Set path to the execution results
 
 listOfDatabase <- fs::dir_ls(resultsPath) %>% # List the databases used in the execution
   basename()
@@ -920,7 +920,7 @@ for (i in 1:length(listOfDatabase)) {
 
   listOfFiles <- list.files(path, full.names = FALSE, pattern = ".rds", recursive = TRUE)
 
-  inputPath <- here::here("results_0603", db, listOfTasks[11])
+  inputPath <- here::here("results", db, listOfTasks[11])
 
   fs::file_copy(here::here(inputPath, listOfFiles),
                 here::here(outputPath, listOfFiles), overwrite = TRUE)
@@ -945,7 +945,7 @@ for (i in 1:length(listOfDatabase)) {
 
   listOfFiles <- list.files(path, full.names = FALSE, pattern = ".rds", recursive = TRUE)
 
-  inputPath <- here::here("results_0603", db, listOfTasks[12])
+  inputPath <- here::here("results", db, listOfTasks[12])
 
   fs::file_copy(here::here(inputPath, listOfFiles),
                 here::here(outputPath, listOfFiles), overwrite = TRUE)
@@ -1000,7 +1000,7 @@ for (i in 1:length(listOfDatabase)) {
 
   listOfFiles <- list.files(path, full.names = FALSE, pattern = ".rds", recursive = TRUE)
 
-  inputPath <- here::here("results_0603", db, listOfTasks[14])
+  inputPath <- here::here("results", db, listOfTasks[14])
 
   fs::file_copy(here::here(inputPath, listOfFiles),
                 here::here(outputPath, listOfFiles), overwrite = TRUE)

diff --git a/shiny/migration/helpers.R b/shiny/migration/helpers.R
@@ -430,12 +430,6 @@ getSurvProbTab <- function(kmData,
 }
 
 
-#test
-# getSurvProbTab(kmData = kmData,
-#                targetCohortId = 1L,
-#                database = "cprdAurum",
-#                era = "era_30")
-
 getTimeTab <- function(kmData,
                        targetCohortId, # select target cohort
                        database, # select database
@@ -479,8 +473,3 @@ getTimeTab <- function(kmData,
   return(timeTab)
 }
 
-
-# getTimeTab(kmData = kmData,
-#            targetCohortId = 1L,
-#            database = "cprdAurum",
-#            era = "era_30")